Research workbench
Structural analysis of inositol monophosphatase complexes with substrates
Analyse Structural analysis of inositol monophosphatase complexes with substrates in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IMA
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inositol monophosphatase
- EC
- 3.1.3.25
- UniProt
- P29218
- Ligands
- IPD, GD
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Inositol monophosphatase (EC 3.1.3.25) | protein | 272 | 36% helix, 25% strand | P29218 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 2 copies · chains A, B
- GD · Gadolinium atom · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.78 | 0.87 | 57 | IPD |
| 2 | 419 | 0.77 | 0.86 | 56 | IPD |
| 3 | 504 | 0.61 | 0.74 | 52 | empty |
| 4 | 120 | 0.45 | 0.77 | 16 | empty |
| 5 | 129 | 0.41 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1714 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1IMA · Structural analysis of inositol monophosphatase complexes with substrates · the same entry in another collection · chain A against A, TM-score 1.00
- P29218 · AlphaFold monomer V2.0 prediction for inositol monophosphatase 1 (P29218) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P29218
- Elsewhere: RCSB PDB 1IMA · PDBe 1IMA · UniProt P29218
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